Genome-wide identification, characterization and expression of C2H2 zinc finger gene family in Opisthopappus species under salt stress.

BACKGROUND: The C2H2 zinc finger protein family plays important roles in plants. However, precisely how C2H2s function in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear. RESULTS: In this study, a total of 69 OpC2H2 zinc finger protein genes were identified and clustered into five Groups. Seven tandem and ten fragment repeats were found in OpC2H2s, which underwent robust purifying selection. Of the identified motifs, motif 1 was present in all OpC2H2s and conserved at important binding sites. Most OpC2H2s possessed few introns and exons that could rapidly activate and react when faced with stress. The OpC2H2 promoter sequences mainly contained diverse regulatory elements, such as ARE, ABRE, and LTR. Under salt stress, two up-regulated OpC2H2s (OpC2H2-1 and OpC2H2-14) genes and one down-regulated OpC2H2 gene (OpC2H2-7) might serve as key transcription factors through the ABA and JA signaling pathways to regulate the growth and development of Opisthopappus species. CONCLUSION: The above results not only help to understand the function of C2H2 gene family but also drive progress in genetic improvement for the salt tolerance of Opisthopappus species.

Identification and expression analysis of XIP gene family members in rice.

Xylanase inhibitor proteins (XIP) are widely distributed in the plant kingdom, and also exist in rice. However, a systematic bioinformatics analysis of this gene family in rice (OsXIP) has not been conducted to date. In this study, we identified 32 members of the OsXIP gene family and analyzed their physicochemical properties, chromosomal localization, gene structure, protein structure, expression profiles, and interaction networks. Our results indicated that OsXIP genes exhibit an uneven distribution across eight rice chromosomes. These genes generally feature a low number of introns or are intronless, all family members, except for OsXIP20, contain two highly conserved motifs, namely Motif 8 and Motif 9. In addition, it is worth noting that the promoter regions of OsXIP gene family members feature a widespread presence of abscisic acid response elements (ABRE) and gibberellin response elements (GARE-motif and TATC-box). Quantitative Real-time PCR (qRT-PCR) analysis unveiled that the expression of OsXIP genes exhibited higher levels in leaves and roots, with considerable variation in the expression of each gene in these tissues both prior to and following treatments with abscisic acid (ABA) and gibberellin (GA3). Protein interaction studies and microRNA (miRNA) target prediction showed that OsXIP engages with key elements within the hormone-responsive and drought signaling pathways. The qRT-PCR suggested osa-miR2927 as a potential key regulator in the rice responding to drought stress, functioning as tissue-specific and temporally regulation. This study provides a theoretical foundation for further analysis of the functions within the OsXIP gene family.

Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress.

Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain cliff-dwelling species. Using RNA-seq data, differentially expressed genes (DEGs) were identified under time and concentration gradients of salt stress. Two types of AS, skipped exon (SE) and mutually exclusive exons (MXE), were found. Differentially alternative splicing (DAS) genes in both species were significantly enriched in "protein phosphorylation", "starch and sucrose metabolism", and "plant hormone signal transduction" pathways. Meanwhile, distinct GO terms and KEGG pathways of DAS occurred between two species. Only a small subset of DAS genes overlapped with DEGs under salt stress. Although both species likely adopted protein phosphorylation to enhance salt stress tolerance, they exhibited distinct responses. The results indicated that the salt stress mechanisms of both Opisthopappus species exhibited similarities and differences in response to salt stress, which suggested that adaptive divergence might have occurred between them. This study initially provides a comprehensive description of salt responsive AS events in Opisthopappus and conveys some insights into the molecular mechanisms behind species tolerance on the Taihang Mountains.

Identification and Analysis of lncRNA and circRNA Related to Wheat Grain Development.

The role of lncRNA and circRNA in wheat grain development is still unclear. The objectives of this study were to characterize the lncRNA and circRNA in the wheat grain development and to construct the interaction network among lncRNA, circRNA, and their target miRNA to propose a lncRNA-circRNA-miRNA module related to wheat grain development. Full transcriptome sequencing on two wheat varieties (Annong 0942 and Anke 2005) with significant differences in 1000-grain weight at 10 d (days after pollination), 20 d, and 30 d of grain development were conducted. We detected 650, 736, and 609 differentially expressed lncRNA genes, and 769, 1054, and 1062 differentially expressed circRNA genes in the grains of 10 days, 20 days and 30 days after pollination between Annong 0942 and Anke 2005, respectively. An analysis of the lncRNA-miRNA and circRNA-miRNA targeting networks reveals that circRNAs exhibit a more complex and extensive interaction network in the development of cereal grains and the formation of grain shape. Central to these interactions are tae-miR1177, tae-miR1128, and tae-miR1130b-3p. In contrast, lncRNA genes only form a singular network centered around tae-miR1133 and tae-miR5175-5p when comparing between varieties. Further analysis is conducted on the underlying genes of all target miRNAs, we identified TaNF-YB1 targeted by tae-miR1122a and TaTGW-7B targeted by miR1130a as two pivotal regulatory genes in the development of wheat grains. The quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays confirmed the target regulatory relationships between miR1130a-TaTGW-7B and miR1122a-TaNF-YB1. We propose a network of circRNA and miRNA-mediated gene regulation in the development of wheat grains.

Molecular prospective on the wheat grain development.

Wheat grain development is an important biological process to determine grain yield and quality, which is controlled by the interplay of genetic, epigenetic, and environmental factors. Wheat grain development has been extensively characterized at the phenotypic and genetic levels. The advent of innovative molecular technologies allows us to characterize genes, proteins, and regulatory factors involved in wheat grain development, which have enhanced our understanding of the wheat seed development process. However, wheat is an allohexaploid with a large genome size, the molecular mechanisms underlying the wheat grain development have not been well understood as those in diploids. Understanding grain development, and how it is regulated, is of fundamental importance for improving grain yield and quality through conventional breeding or genetic engineering. Herein, we review the current discoveries on the molecular mechanisms underlying wheat grain development. Notably, only a handful of genes that control wheat grain development have, thus far, been well characterized, their interplay underlying the grain development remains elusive. The synergistic network-integrated genomics and epigenetics underlying wheat grain development and how the subgenome divergence dynamically and precisely regulates wheat grain development are unknown.

Conjunctive Analyses of BSA-Seq and BSR-Seq to Identify Candidate Genes Controlling the Black Lemma and Pericarp Trait in Barley.

Black barley seeds are a health-beneficial diet resource because of their special chemical composition and antioxidant properties. The black lemma and pericarp (BLP) locus was mapped in a genetic interval of 0.807 Mb on chromosome 1H, but its genetic basis remains unknown. In this study, targeted metabolomics and conjunctive analyses of BSA-seq and BSR-seq were used to identify candidate genes of BLP and the precursors of black pigments. The results revealed that five candidate genes, purple acid phosphatase, 3-ketoacyl-CoA synthase 11, coiled-coil domain-containing protein 167, subtilisin-like protease, and caffeic acid-O-methyltransferase, of the BLP locus were identified in the 10.12 Mb location region on the 1H chromosome after differential expression analysis, and 17 differential metabolites, including the precursor and repeating unit of allomelanin, were accumulated in the late mike stage of black barley. Phenol nitrogen-free precursors such as catechol (protocatechuic aldehyde) or catecholic acids (caffeic, protocatechuic, and gallic acids) may promote black pigmentation. BLP can manipulate the accumulation of benzoic acid derivatives (salicylic acid, 2,4-dihydroxybenzoic acid, gallic acid, gentisic acid, protocatechuic acid, syringic acid, vanillic acid, protocatechuic aldehyde, and syringaldehyde) through the shikimate/chorismite pathway other than the phenylalanine pathway and alter the metabolism of the phenylpropanoid-monolignol branch. Collectively, it is reasonable to infer that black pigmentation in barley is due to allomelanin biosynthesis in the lemma and pericarp, and BLP regulates melanogenesis by manipulating the biosynthesis of its precursors.

Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains.

Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.

N6-Methyladenosine dynamic changes and differential methylation in wheat grain development.

MAIN CONCLUSION: More methylation changes occur in late interval than in early interval of wheat seed development with protein and the starch synthesis-related pathway enriched in the later stages. Wheat seed development is a critical process to determining wheat yield and quality, which is controlled by genetics, epigenetics and environments. The N6-methyladenosine (m6A) modification is a reversible and dynamic process and plays regulatory role in plant development and stress responses. To better understand the role of m6A in wheat grain development, we characterized the m6A modification at 10 day post-anthesis (DPA), 20 DPA and 30 DPA in wheat grain development. m6A-seq identified 30,615, 30,326, 27,676 high confidence m6A peaks from the 10DPA, 20DPA, and 30DPA, respectively, and enriched at 3'UTR. There were 29,964, 29,542 and 26,834 unique peaks identified in AN0942_10d, AN0942_20d and AN0942_30d. One hundred and forty-two genes were methylated by m6A throughout seed development, 940 genes methylated in early grain development (AN0942_20d vs AN0942_10d), 1542 genes in late grain development (AN0942_30d vs AN0942_20d), and 1190 genes between early and late development stage (AN0942_30d vs AN0942_10d). KEGG enrichment analysis found that protein-related pathways and the starch synthesis-related pathway were significantly enriched in the later stages of seed development. Our results provide novel knowledge on m6A dynamic changes and its roles in wheat grain development.

N 6-Methyladenosine and physiological response divergence confer autotetraploid enhanced salt tolerance compared to its diploid Hordeum bulbosum.

Polyploid species have played an essential role in plant evolution, exemplified by adaptive advantages to abiotic stress. N 6-Methyladenosine (m6A) is suggested to play an important role in stress response. However, whether genome doubling affects m6A to increase autopolyploids stress tolerance is still unclear. This study aims to compare physiological (maintaining osmoregulatory homeostasis) and m6A changes between autotetraploid and diploid wild barley (Hordeum bulbosum) in response to salt (NaCl) stress. Results showed that autotetraploids physiologically had enhanced stress tolerance based on the measured parameters of relative water content, water loss, proline, H2O2, and chlorophyll. Diploid H. bulbosum experienced an excessive abundance of proline following salt stress where tetraploids had beneficial proline accumulation and thus enhanced osmoregulation. The significantly higher level of proline and H2O2 in diploid than in autotetraploid implies that diploids suffered higher osmotic stress than autotetraploid. Autotetraploid produced enough proline to protect stress, but not so much to cause toxicity. m6A in total RNA showed no significant difference between ploidies in controls, but was significantly higher in autotetraploids than in diploids during stress and recovery. These results suggest that increased m6A might be one of molecular mechanisms that increases salt tolerance in autotetraploid H. bulbosum compared to diploids, which enhances the adaptation of autopolyploids. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01260-x.

Origins and chromosome differentiation of Thinopyrum elongatum revealed by PepC and Pgk1 genes and ND-FISH.

Thinopyrum elongatum is an important gene pool for wheat genetic improvement. However, the origins of the Thinopyrum genomes and the nature of the genus' intraspecific relationships are still controversial. In this study, we used single-copy nuclear genes and non-denaturing fluorescence in situ hybridization (ND-FISH) to characterize genome constitution and chromosome differentiation in Th. elongatum. According to phylogenetic analyses based on PepC and Pgk1 genes, there was an E genome with three versions (Ee, Eb, Ex) and St genomes in the polyploid Th. elongatum. The ND-FISH results of pSc119.2 and pAs1 revealed that the karyotypes of diploid Th. elongatum and Th. bessarabicum were different, and the chromosome differentiation occurred among accessions of the diploid Th. elongatum. In addition, the tetraploid Th. elongatum has two groups of ND-FISH karyotype, indicating that the tetraploid Th. elongatum might be a segmental allotetraploid. In summary, our results suggested that the diploid Th. elongatum, Th. Bessarabicum, and Pseudoroegneria were the donors of the Ee, Eb, and St genomes to the polyploid Th. elongatum, respectively.

Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus).

BACKGROUND: Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS: Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS: Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.

MicroRNA-mediated responses to colchicine treatment in barley.

MAIN CONCLUSION: In Hordeum vulgare, nine differentially expressed novel miRNAs were induced by colchicine. Five novel miRNA in colchicine solution showed the opposite expression patterns as those in water. Colchicine is a commonly used agent for plant chromosome set doubling. MicroRNA-mediated responses to colchicine treatment in plants have not been characterized. Here, we characterized new microRNAs induced by colchicine treatment in Hordeum vulgare using high-throughput sequencing. Our results showed that 39 differentially expressed miRNAs were affected by water treatment, including 34 novel miRNAs and 5 known miRNAs; 42 miRNAs, including 37 novel miRNAs and 5 known miRNAs, were synergistically affected by colchicine and water, and 9 differentially expressed novel miRNAs were induced by colchicine. The novel_mir69, novel_mir57, novel_mir75, novel_mir38, and novel_mir56 in colchicine treatment showed the opposite expression patterns as those in water. By analyzing these 9 differentially expressed novel miRNAs and their targets, we found that novel_mir69, novel_mir56 and novel_mir25 co-target the genes involving the DNA repair pathway. Based on our results, microRNA-target regulation network under colchicine treatment was proposed, which involves actin, cell cycle regulation, cell wall synthesis, and the regulation of oxidative stress. Overall, the results demonstrated the critical role of microRNAs mediated responses to colchicine treatment in plants.

Evolutionary patterns of plastome uncover diploid-polyploid maternal relationships in Triticeae.

To investigate the diploid-polyploid relationships and the role of maternal progenitors in establishment of polyploid richness in Triticeae, 35 polyploids representing almost all genomic constitutions together with 48 diploid taxa representing 20 basic genomes in the tribe were analyzed. Phylogenomic reconstruction, genetic distance matrix, and nucleotide diversity patterns of plastome sequences indicated that (1) The maternal donor of the annual polyploid species with the U- and D-genome are related to extant Ae. umbellulata and Ae. tauschii, respectively. The maternal donor to the annual polyploid species with the S-, G-, and B-genome originated from the species of Sitopsis section of the genus Aegilops. The annual species with the Xe-containing polyploids were donated by Eremopyrum as the female parent; (2) Pseudoroegneria and Psathyrostachys were the maternal donor of perennial species with the St- and Ns-containing polyploids, respectively; (3) The Lophopyrum, Thinopyrum and Dasypyrum genomes contributed cytoplasm genome to Pseudoroegneria species as a result of incomplete lineage sorting and/or chloroplast captures, and these lineages were genetically transmitted to the St-containing polyploid species via polyploidization; (4) There is a reticulate relationship among the St-containing polyploid species. It can be suggested that genetic heterogeneity might associate with the richness of the polyploids in Triticeae.

Insights into the N6-methyladenosine mechanism and its functionality: progress and questions.

N6-methyladenosine (m6A) RNA methylation has become a progressively popular area of molecular research since the discovery of its potentially essential regulatory role amongst eukaryotes. m6A marks are observed in the 5'UTR, 3'UTR and coding regions of eukaryotes and its mediation has been associated with various human diseases, RNA stability and translational efficiency. To understand the implications of m6A methylation in molecular governance, its functionality and mechanism must be initially understood. m6A regulation through its readers, writers and erasers as well as an insight into the potential "cross-talk" occurring between m6A and previously well documented regulatory molecular mechanisms have been characterized. The majority of research to date has been limited to few species and has yet to explore the species- and tissue specific nature or mechanistic plasticity of m6A regulation. There is still a tremendous gap in our knowledge surrounding the mechanism and functionality of m6A RNA methylation. Here we review the formation, removal, and decoding of m6A amongst animals, yeast, and plants while noting potential "cross-talk" between various mechanisms and highlighting potential areas of future research.

Genome constitution and evolution of Elytrigia lolioides inferred from Acc1, EF-G, ITS, TrnL-F sequences and GISH.

BACKGROUND: Elytrigia lolioides (Kar. et Kir.) Nevski, which is a perennial, cross-pollinating wheatgrass that is distributed in Russia and Kazakhstan, is classified into Elytrigia, Elymus, and Lophopyrum genera by taxonomists on the basis of different taxonomic classification systems. However, the genomic constitution of E. lolioides is still unknown. To identify the genome constitution and evolution of E. lolioides, we used single-copy nuclear genes acetyl-CoA carboxylase (Acc1) and elongation factor G (EF-G), multi-copy nuclear gene internal transcribed space (ITS), chloroplast gene trnL-F together with fluorescence and genomic in situ hybridization. RESULTS: Despite the widespread homogenization of ITS sequences, two distinct lineages (genera Pseudoroegneria and Hordeum) were identified. Acc1 and EF-G sequences suggested that in addition to Pseudoroegneria and Hordeum, unknown genome was the third potential donor of E. lolioides. Data from chloroplast DNA showed that Pseudoroegneria is the maternal donor of E. lolioides. Data from specific FISH marker for St genome indicated that E. lolioides has two sets of St genomes. Both genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) results confirmed the presence of Hordeum genome in this species. When E genome was used as the probe, no signal was found in 42 chromosomes. The E-like copy of Acc1 sequences was detected in E. lolioides possibly due to the introgression from E genome species. One of the H chromosomes in the accession W6-26586 from Kazakhstan did not hybridize H genome signals but had St genome signals on the pericentromeric regions in the two-color GISH. CONCLUSIONS: Phylogenetic and in situ hybridization indicated the presence of two sets of Pseudoroegneria and one set of Hordeum genome in E. lolioides. The genome formula of E. lolioides was designed as StStStStHH. E. lolioides may have originated through the hybridization between tetraploid Elymus (StH) and diploid Pseudoroegneria species. E and unknown genomes may participate in the speciation of E. lolioides through introgression. According to the genome classification system, E. lolioides should be transferred into Elymus L. and renamed as Elymus lolioidus (Kar. er Kir.) Meld.

Transcriptome and miRNAs analyses enhance our understanding of the evolutionary advantages of polyploidy.

Polyploid organisms have more than two sets of chromosomes, including autopolyploid via intraspecific genome doubling, and allopolyploid via merging genomes of distinct species by hybridization. Polyploid organisms are widespread in plants, indicating that polyploidy has some evolutionary advantages over its diploid ancestor. Actually, polyploidy is always tightly associated with hybrid vigor and adaptation to adverse environmental conditions. However, why polyploidy can develop such advantages is poorly known. MicroRNAs (miRNAs) are endogenous ∼21 nt small RNAs which can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. MicroRNAs are essential for cell development, differentiation, signal transduction, and show an adaptive response to biotic and abiotic stresses. Environmental stresses cause plants to over- or under-express certain miRNAs or synthesize new miRNAs to cope with stress. We have here reviewed our current knowledge on the molecular mechanisms, which can account for the evolutionary advantages of polyploidy over its diploid ancestor from genome-wide gene expression and microRNAs expression perspectives.

microRNAs contribute to enhanced salt adaptation of the autopolyploid Hordeum bulbosum compared with its diploid ancestor.

Several studies have shown that autopolyploid can tolerate abiotic stresses better than its diploid ancestor. However, the underlying molecular mechanism is poorly known. microRNAs (miRNAs) are small RNAs that regulate the target gene expression post-transcriptionally and play a critical role in the response to abiotic stresses. Duplication of the whole genome can result in the expansion of miRNA families, and the innovative miRNA-target interaction is important for adaptive responses to various environments. We identified new microRNAs induced by genome duplication, that are also associated with stress response and the distinctive microRNA networks in tetraploid and diploid Hordeum bulbosum using high-throughput sequencing. Physiological results showed that autotetraploid Hordeum bulbosum tolerated salt stress better than its diploid. Comparison of miRNAs expression between diploid and tetraploid check (CK) and salt stress revealed that five miRNAs affected by genome doubling were also involved in salt stress response. Of these, miR528b-3p was only detected in the tetraploid, and downregulated under salt stress relative to that in tetraploid CK. Moreover, through target prediction, it was found that miR528b-3p was not only involved in DNA replication and repair but also participated in salt stress response. Finally, by analyzing all the differentially expressed microRNAs and their targets, we also discovered distinguished microRNAs-target regulatory networks in diploid and tetraploid, respectively. Overall, the results demonstrated the critical role of microRNAs in autopolyploid to have better tolerance salt stress.

Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat.

BACKGROUND: 337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory function of MicroRNAs (miRNAs) in reproductive development has been increasingly studied, their roles in pre-meiotic and meiotic cells formation of plants have not been clearly explored. Here, we explored the roles of miRNAs in regulating male sterility of 337S at short day length/low temperature condition. RESULTS: Small RNA sequencing and degradome analyses were employed to identify miRNAs and their targets in the 337S whose meiotic cells collapsed rapidly during male meiotic prophase, resulting in failure of meiosis at SL condition. A total of 102 unique miRNAs were detected. Noticeably, the largest miRNA family was MiR1122. The target CCR4-associated factor 1 (CAF1) of miR2275, a subunit of the Carbon Catabolite Repressed 4-Negative on TATA-less (CCR4-NOT) complex, contributes to the process of early meiosis, and was first identified here. Further studies showed that the expression of several pivotal anther-related miRNAs was altered in 337S at SL condition, especially tae-miR1127a, which may be related to male sterility of 337S. Here, we also identified a new member of SWI/SNF factors SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A, member 3-like 3 (SMARCA3L3) targeted by tae-miR1127a, whose function might be involved in faithful progression of meiosis in male reproductive cells. CONCLUSION: The miRNA-target interactions of tae-miR2275-CAF1 and tae-miR1127a-SMARCA3L3 might be involved in regulating male fertility in 337S. Our results also implied that multiple roles for SMARCA3L3 and CAF1 in DNA repair and transcriptional regulation jointly orchestrated a tight and orderly system for maintaining chromatin and genome integrity during meiosis.

Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition.

BACKGROUND: Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions. Of them, leaf age (LAG), shoot height (SH), maximum root length (MRL), main root number (MRN) and seedling fresh weight (SFW) were investigated at the 13th, 20th, 27th, and 34th day after germination. The objectives were to identify quantitative trait loci (QTLs) underlying these seedling characteristics using a high-density linkage map and to reveal the QTL expression pattern by comparing the QTLs among four different seedling growth stages. RESULTS: A total of 70 QTLs were distributed over all chromosomes except 4H, and, individually, accounted for 5.01%-77.78% of phenotypic variation. Out of the 70 detected QTLs, 23 showed a major effect on 14 seedling-related characteristics. Ten co-localized chromosomal regions on 2H (five regions), 3H (two regions) and 7H (three regions) involved 39 QTLs (55.71%), each simultaneously influenced more than one trait. Meanwhile, 9 co-localized genomic regions involving 22 QTLs for five seedling characteristics (LAG, SH, MRL, MRN and SFW) at the 13th, 20th, 27th and 34th day-old seedling were common for two or more growth stages of seedling. QTL in the vicinity of Vrs1 locus on chromosome 2H with the favorable alleles from Huadamai 6 was found to have the largest main effects on multiple seedling-related traits. CONCLUSIONS: Six QTL cluster regions associated with 16 seedling-related characteristics were observed on chromosome 2H, 3H and 7H. The majority of the 29 regions identified for five seedling characteristics were selectively expressed at different developmental stages. The genetic effects of 9 consecutive expression regions displayed different developmental influences at different developmental stages. These findings enhanced our understanding of a genetic basis underlying seedling characteristics in barley. Some QTLs detected here could be used for marker-assisted selection (MAS) in barley breeding.

Phylogenetic analysis of two single-copy nuclear genes revealed origin and complex relationships of polyploid species of Hordeum in Triticeae (Poaceae).

Two single-copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and thioredoxin-like gene (HTL), were used to explore the phylogeny and origin of polyploid species in Hordeum. Our results were partly in accord with previous studies, but disclosed additional complexity. Both RPB2 and HTL trees confirmed the presence of Xa genome in H. capense and H. secalinum, and that H. depressum originated from H. californicum together with other American diploids, either H. intercedens or H. pusillum. American diploids solely contributed to the origin of H. depressum. The Asian diploids, either H. bogdanii or H. brevisubulatum, contributed to the formation of American polyploids except H. depressum. RPB2 and HTL sequences showed that H. roshevitzii did not contribute to the origin of American tetraploids. Our data showed a close relationship between the hexaploids H. procerum and H. parodii and the tetraploids H. brachyantherum, H. fuegianum, H. guatemalense, H. jubatum, and H. tetraploidum. The involvement of the diploid H. pusillum and the tetraploid H. jubatum in the formation of H. arizonicum was also indicated in the HTL phylogeny. Our results suggested a possible gene introgression of W- and P-genome species into the tetraploid H. jubatum and the hexaploid H. procerum.